ArticleNature protocols2012
Nicking enzyme-based internal labeling of DNA at multiple loci.
Article in Nature protocols, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed.
- DNA Bioconjugation with Polymer Beads Using SNAP-tag® Technology.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The SMC Hinge is a Selective Gate for Obstacle Bypass.Nature communications · 2025Article
- Structural and mechanistic insights into the sequential dsDNA cleavage by SpCas12f1.Nucleic acids research · 2025Article
- A high-throughput single-molecule platform to study DNA supercoiling effect on protein-DNA interactions.Nucleic acids research · 2025Article
- DNA supercoiling-mediated G4/R-loop formation tunes transcription by controlling the access of RNA polymerase.Nature communications · 2025Article
- Mechanism of DNA unwinding by MCM8-9 in complex with HROB.Nature communications · 2024Article
- Innate programmable DNA binding by CRISPR-Cas12m effectors enable efficient base editing.Nucleic acids research · 2024Article
- De novo fabrication of custom-sequence plasmids for the synthesis of long DNA constructs with extrahelical features.Biophysical journal · 2024Article
- Mechanism of DNA unwinding by hexameric MCM8-9 in complex with HROB.Research square · 2023Article
- A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex.Nature communications · 2022Article
- Probing the stability of the SpCas9-DNA complex after cleavage.Nucleic acids research · 2021Article
- Detection of base analogs incorporated during DNA replication by nanopore sequencing.Nucleic acids research · 2020Article
- Chemical roadblocking of DNA transcription for nascent RNA display.The Journal of biological chemistry · 2020Article
- Competing interaction partners modulate the activity of Sgs1 helicase during DNA end resection.The EMBO journal · 2019Article
- Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA.Biophysical journal · 2019Article
- Supercoiling DNA Locates Mismatches.Physical review letters · 2017Article
- Efficient modification of λ-DNA substrates for single-molecule studies.Scientific reports · 2017Article
- Fluorescently labeled circular DNA molecules for DNA topology and topoisomerases.Scientific reports · 2016Article
- Force regulated dynamics of RPA on a DNA fork.Nucleic acids research · 2016Article
- Cationic Polymer Intercalation into the Lipid Membrane Enables Intact Polyplex DNA Escape from Endosomes for Gene Delivery.Molecular pharmaceutics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The labeling of biomolecules has become standard practice in molecular biosciences. Modifications are used for detection, sorting and isolation of small molecules, complexes and entire cells. We have recently reported a method for introducing internal chemical and structural modifications into kbp-sized DNA target substrates that are frequently used in single-molecule experiments. It makes use of nicking enzymes that create single-stranded DNA gaps, which can be subsequently filled with labeled oligonucleotides. Here we provide a detailed protocol and further expand this method. We show that modifications can be introduced at distant loci within one molecule in a simple one-pot reaction. In addition, we achieve labeling on both strands at a specific locus, as demonstrated by Förster resonance energy transfer (FRET) experiments. The protocol requires an initial cloning of the target substrate (3-5 d), whereas the labeling itself takes 4-6 h. More elaborate purification and verification of label incorporation requires 2 h for each method.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.